SNP Cutter: SNP PCR-RFLP Assay Design                                              SNP Cutter FAQ

SNP Cutter Workflow Diagram

SNP_Cutter Input and Output Examples

* entries are required

1. * List of dbSNP rs IDs  (must be prefixed with "rs", as rs125, one ID per line) or SNPs with flanking sequence in specified format(Temporarily, if rs IDs are used as input, only 20 or less SNPs could be processed each time due to BLAT restriction at Genome Browser. No such restriction apply for the input of formatted sequences longer than the maximum PCR product size. SNPSequer for SNP sequence preparation is under renovation to remove this restriction. )

or upload data file

 Input data type: (Note: data can not be processed without correct data type identification. "SNP sequences data" is preferred for efficient data processing.)

 Additional flanking sequences can be extracted by using , if the SNP flanking sequence was too short in the supplied data.

   (MediumMode or SlowMode is suggested for SNPs that failed to work with FastMode.  Refer to SNP mapping function for the meaning of different types of modes.)

2. Output filename label: (Please use one word comprised of only alphabets)

3. * Restriction Enzyme (RE) list:

    REBASE enzymes
    Inexpensive enzymes
    Efficient/reliable enzymes (used in publications)
    User's own restriction enzyme list (format identical to the above restriction enzyme list):

4. * For mismatched PCR-RFLPs, a base perfect match is required at the 3' end of the primer.

5. Adjustable parameters for Primer 3:    (Primer3's internal parameters use the default value)

   1)For natural PCR-RFLPs:

  2)For mismatch PCR-RFLPs:

6. Choice of outputs:

7. Email address to which the results will be mailed to:

Email address * 

8. Choice of gzip compression for output data:

9. Choice of email:

Email attachment size limit:

Check this box , if your input data file is from a Mac machine,

Submit efficient enzymes

After Primers are designed, designs can be checked by:

By Ruifang Zhang, Zanhua Zhu, Fengxia Yao, Hongming Zhu, Tu Nguyen, Chunyu Liu